R Notebook

rr seurobj <- readRDS(‘output/seurat_objects/180831/10x-180831’)

Colors

rr hcl_palettes(plot = TRUE)

Timepoint colors

plot_grid(
  TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=rev(sequential_hcl(5, palette='TealGrn'))),
  TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=rev(sequential_hcl(5, palette='BluGrn'))),
  TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=rev(sequential_hcl(5, palette='Blue Yellow'))),
  TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=rev(sequential_hcl(5, palette='PurpOr')))
)

Custom colors timepoints

plot_grid(
  TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=rev(c('#0263A1', '#008FB0', '#4CB6BC', '#8ED7CA', '#CBF1DE'))),
  TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=rev(c('#4847A1', '#0087BE', '#00BED1', '#3DEFDA', '#B0FFDF'))),
  TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=rev(c('#00589C','#008DA5', '#00B9A1', '#6DDD95', '#D7F797'))),
  TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=rev(c('#0077B5', '#00A7C3', '#00CAC2', '#42E0B4', '#8CE599'))),
  TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=rev(c('#005090','#007C98','#00A39B','#00C598','#86E094'))),
   TSNEPlot(seurobj, group.by='timepoint', pt.size=1, colors.use=c('#f5eb82','#c8d29b','#bca986','#bf877f','#a8cec2')), ncol=2, labels=c('custom1', 'custom2', 'custom3', 'custom4', 'custom5', 'custom6')
)

Depots

plot_grid(
  TSNEPlot(seurobj, group.by='depot', pt.size=1, colors.use=c('#825c2a', '#ebd1ac', '#5c3724', '#eab476')),
  TSNEPlot(seurobj, group.by='depot', pt.size=1, colors.use=c('#82643a', '#d1a567', '#6c4431', '#e3c78a')),
  TSNEPlot(seurobj, group.by='depot', pt.size=1, colors.use=c('#825c2a', '#ebd1ac', '#5c3724', '#d1a567')),
  TSNEPlot(seurobj, group.by='depot', pt.size=1, colors.use=c('brown', 'orange', '#5c3724', '#d1a567')),
  ncol=2
)

Monocle

rr cds <- readRDS(‘output/monocle/180831/monocle_T1T2T3_T4T5_res1.5/10x-180831-monocle-metadata’)

plot_grid(
  plot_cell_trajectory(cds, color_by='timepoint') + scale_color_manual(values=rev(c('#0077B5', '#00A7C3', '#00CAC2', '#42E0B4', '#8CE599')), name = "Timepoint"),
  plot_cell_trajectory(cds, color_by='timepoint') + geom_point(color='white', size=5) + geom_point(aes(colour=timepoint), alpha=0.1) + scale_color_manual(values=rev(c('#0077B5', '#00A7C3', '#00CAC2', '#42E0B4', '#8CE599')), name = "Timepoint"),
  plot_cell_trajectory(cds, color_by='timepoint') + scale_color_manual(values=rev(sequential_hcl(5, palette='TealGrn')), name = "Timepoint"),
  plot_cell_trajectory(cds, color_by='timepoint') + geom_point(color='white', size=5) + geom_point(aes(colour=timepoint), alpha=0.1) + scale_color_manual(values=rev(sequential_hcl(5, palette='TealGrn')), name = "Timepoint"),
  plot_cell_trajectory(cds),
  plot_cell_trajectory(cds) + scale_color_manual(values=c('#fbea7d', '#e27268', '#7ba2c3'), name='State'),
  plot_cell_trajectory(cds, color_by='type') + scale_color_manual(values=c('#825c2a', '#ebd1ac'), name='Type'),
  plot_cell_trajectory(cds, color_by='depot') + scale_color_manual(values=c('#82643a', '#d1a567', '#6c4431', '#e3c78a'), name='Depot'),
  ncol=2
)

Monocle predictions in Seurat tSNE

Final figures